1GA5

CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

DNA Deformability as a Recognition Feature in the RevErb Response Element

Sierk, M.L.Zhao, Q.Rastinejad, F.

(2001) Biochemistry 40: 12833-12843

  • Primary Citation of Related Structures:  1HLZ

  • PubMed Abstract: 
  • Most nuclear receptors recognize the same consensus hexameric sequence, AGGTCA. An important question has been how the various members of this transcription factor family distinguish identity features in these closely related DNA sites. We determined ...

    Most nuclear receptors recognize the same consensus hexameric sequence, AGGTCA. An important question has been how the various members of this transcription factor family distinguish identity features in these closely related DNA sites. We determined structures from several crystal forms of the RevErb-DNA complex and analyzed the patterns of protein-DNA interactions and DNA distortions. We found a significant and consistent DNA distortion at a TA step directly preceding the first consensus 5'-AGGTCA-3' recognition sequence. Importantly, while this base-pair sequence is associated with RevErb's high-affinity sites, there are no sequence-specific contacts formed with the protein. Our study shows that RevErb relies instead on the intrinsic geometry and flexibility of this TA site to make the required fit between the proteins' independent major groove and minor groove binding interactions, which occur on both sides of the TA step. Our findings extend the description of response element discrimination to include a role for sequence-dependent DNA deformations and suggest how other monomeric members of this superfamily, such as NGFI-B, SF-1, and ROR, could also recognize unique geometric features in their DNA targets.


    Related Citations: 
    • Structural Elements of an Orphan Nuclear Receptor-DNA Complex
      Zhao, Q.,Khorasanizadeh, S.,Miyoshi, Y.,Lazar, M.,Rastinejad, F.
      (1998) Mol.Cell 1: 849


    Organizational Affiliation

    Department of Pharmacology, University of Virginia, Charlottesville, Virginia 22908-0735, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ORPHAN NUCLEAR RECEPTOR NR1D1
A, B, E, F
94Homo sapiensGene Names: NR1D1 (EAR1, HREV, THRAL)
Find proteins for P20393 (Homo sapiens)
Go to Gene View: NR1D1
Go to UniProtKB:  P20393
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP*AP*G)-3'C,G20N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*(5IT)P*G)-3'D,H20N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5IU
Query on 5IU
D, H
DNA LINKINGC9 H12 I N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.253 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 44.920α = 85.84
b = 52.020β = 76.61
c = 78.880γ = 74.48
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Advisory, Refinement description